[gmx-users] disulfide bond missing even with -ss

Justin Lemkul jalemkul at vt.edu
Sun Jan 21 17:22:57 CET 2018 


On 1/21/18 11:20 AM, MD wrote:
> On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/21/18 10:59 AM, MD wrote:
>>
>>> On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>> On 1/21/18 10:46 AM, MD wrote:
>>>>
>>>> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>> On 1/21/18 10:29 AM, MD wrote:
>>>>>> I modified the specbond.dat and change the cutoff to be 2.04A, still
>>>>>>
>>>>>>> nothing...
>>>>>>>
>>>>>>> Please don't spam the list with minute-by-minute updates.
>>>>>>>
>>>>>> ​
>>>>>>
>>>>> sorry
>>>>> ​for the scattered information, ​
>>>>> I didn't mean to spam the thread..
>>>>>
>>>>>
>>>>>
>>>>> Provide your pdb2gmx command, full screen output, and whatever evidence
>>>>>
>>>>>> you have that the bond wasn't formed. The definitive answer is in your
>>>>>> topology. If it's not there, we can diagnose.
>>>>>>
>>>>>> ​
>>>>>>
>>>>> command line: gmx pdb2gmx -f ncat.pdb -o ncat.gro -water spc -ignh -ss
>>>>>
>>>>>
>>>>>
>>>>> Link CYS-335 SG-2487 and CYS-338 SG-2507 (y/n) ?y
>>>>>
>>>>> There is no indication that anything went wrong, and this should have
>>>> been
>>>> done. Are you saying that there is no line in the topology specifying a
>>>> bond between atoms 2487 and 2507?
>>>>
>>> ​Right. I didn't see anything said about the bond. I went forward to the
>>> step of em.mdp and got a minimized gro, which was converted to pdb. And I
>>> found no disulfide bond in the pdb file.​
>>>
>> So, to be clear, please answer these two questions directly:
>>
>> 1. You find no line in [bonds] in topol_Protein_chain_B.itp file between
>> atoms 2487 and 2507?
>>
> ​Correct.​
>
>
>
>> 2. When you visualize the structure, both Cys335 and Cys338 are in their
>> thiol (-SH) form?
> T
> ​hey are not in thiol form. ​
> ​
> https://docs.google.com/document/d/1HOuMWAylWZOp1KP1cHRp82Y_EiM5xAc8QM5KCAOOkSo/edit?usp=sharing
> ​

This is not consistent with your above assertion. If your structure, 
after pdb2gmx or any point thereafter, does not have -SH, then you are 
modeling a disulfide. You can't simultaneously have no bond defined in 
the topology and also have no thiols. These are mutually exclusive. I 
suspect the bond was formed and you're perhaps looking in the wrong place.

-Justin

>
>
>> -Justin
>>
>>
>>
>>>> -Justin
>>>>
>>>>
>>>> Start terminus THR-24: NH3+
>>>>
>>>>> End terminus LEU-385: COO-
>>>>> Opening force field file ./charmm36-jul2017.ff/merged.arn
>>>>> Checking for duplicate atoms....
>>>>> Generating any missing hydrogen atoms and/or adding termini.
>>>>> Now there are 362 residues with 5724 atoms
>>>>> Chain time...
>>>>>
>>>>> Back Off! I just backed up topol_Protein_chain_B.itp to
>>>>> ./#topol_Protein_chain_B.itp.5#
>>>>> Making bonds...
>>>>> Warning: Long Bond (3206-3204 = 0.339276 nm)
>>>>> Number of bonds was 5800, now 5800
>>>>> Generating angles, dihedrals and pairs...
>>>>> Before cleaning: 15256 pairs
>>>>> Before cleaning: 15446 dihedrals
>>>>> Keeping all generated dihedrals
>>>>> Making cmap torsions...
>>>>> There are  359 cmap torsion pairs
>>>>> There are 15446 dihedrals,  949 impropers, 10509 angles
>>>>>              15142 pairs,     5800 bonds and     0 virtual sites
>>>>> Total mass 40928.695 a.m.u.
>>>>> Total charge -13.000 e
>>>>> Writing topology
>>>>>
>>>>> Back Off! I just backed up posre_Protein_chain_B.itp to
>>>>> ./#posre_Protein_chain_B.itp.5#
>>>>> Processing chain 2 'B' (1 atoms, 1 residues)
>>>>> Warning: Starting residue MG430 in chain not identified as
>>>>> Protein/RNA/DNA.
>>>>> Problem with chain definition, or missing terminal residues.
>>>>> This chain does not appear to contain a recognized chain molecule.
>>>>> If this is incorrect, you can edit residuetypes.dat to modify the
>>>>> behavior.
>>>>> 8 out of 8 lines of specbond.dat converted successfully
>>>>> Opening force field file ./charmm36-jul2017.ff/merged.arn
>>>>> Checking for duplicate atoms....
>>>>> Generating any missing hydrogen atoms and/or adding termini.
>>>>> Now there are 1 residues with 1 atoms
>>>>> Chain time...
>>>>>
>>>>> Back Off! I just backed up topol_Ion_chain_B2.itp to
>>>>> ./#topol_Ion_chain_B2.itp.5#
>>>>> Making bonds...
>>>>> No bonds
>>>>> Generating angles, dihedrals and pairs...
>>>>> Making cmap torsions...
>>>>> There are    0 dihedrals,    0 impropers,    0 angles
>>>>>                 0 pairs,        0 bonds and     0 virtual sites
>>>>> Total mass 24.305 a.m.u.
>>>>> Total charge 2.000 e
>>>>> Writing topology
>>>>>
>>>>> Back Off! I just backed up posre_Ion_chain_B2.itp to
>>>>> ./#posre_Ion_chain_B2.itp.5#
>>>>> Including chain 1 in system: 5724 atoms 362 residues
>>>>> Including chain 2 in system: 1 atoms 1 residues
>>>>> Now there are 5725 atoms and 363 residues
>>>>> Total mass in system 40953.000 a.m.u.
>>>>> Total charge in system -11.000 e
>>>>>
>>>>> Writing coordinate file...
>>>>>
>>>>> Back Off! I just backed up ncat.gro to ./#ncat.gro.5#
>>>>>
>>>>>
>>>>>
>>>>> https://docs.google.com/document/d/1HOuMWAylWZOp1KP1cHRp82Y_
>>>>> EiM5xAc8QM5KCAOOkSo/edit?usp=sharing
>>>>> ​
>>>>>     ​
>>>>>
>>>>>
>>>>> -Justin
>>>>>
>>>>>> On Sun, Jan 21, 2018 at 10:23 AM, MD <refmac5 at gmail.com> wrote:
>>>>>>
>>>>>> I have also tried renaming my two CYS to be CYS2 but no luck either.
>>>>>>> On Sun, Jan 21, 2018 at 10:22 AM, MD <refmac5 at gmail.com> wrote:
>>>>>>>> gromacs did ask me to confirm linking the two cys before the run,
>>>>>>>> but I
>>>>>>>>
>>>>>>>> didn't see any log saying the bond is formed.
>>>>>>>>> On Sun, Jan 21, 2018 at 10:19 AM, MD <refmac5 at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>> Hi Gromacs folks,
>>>>>>>>>
>>>>>>>>> I realized I kept losing disulfide bond after gmx. The length is
>>>>>>>>>> 2.01A
>>>>>>>>>> but I did use -ss when pdb2gmx. Any thoughts?
>>>>>>>>>> Thanks,
>>>>>>>>>> Ming
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Assistant Professor
>>>>>> Virginia Tech Department of Biochemistry
>>>>>>
>>>>>> 303 Engel Hall
>>>>>> 340 West Campus Dr.
>>>>>> Blacksburg, VA 24061
>>>>>>
>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>>>
>>>>>> ==================================================
>>>>>>
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>>>>>> Gromacs Users mailing list
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>>>>>>
>>>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>
>>>> ==================================================
>>>>
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>>>> Gromacs Users mailing list
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>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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